Sunday night's eleventh hour order averted the walkout and left the morning commute to proceed normally, without the widespread travel congestion that a strike involving Bay Area Rapid Transit, the nation's fifth-largest rail line, would have created.
Brown named a board of investigators for a seven-day inquiry into the contract dispute that had labour unions poised to walk off the job at midnight Sunday.
The board called for a public hearing Wednesday in Oakland for both sides to present their arguments.
Brown's order was issued under a decades-old law that allows the state to intervene if a strike will significantly disrupt public transportation services and endanger public health.
It came after BART Board President Tom Radulovich sent a letter to the governor requesting his intervention and a cooling-off period of 60 days, BART spokesman Rick Rice said in a statement.
"For the sake of the people of the Bay Area, I urge — in the strongest terms possible — the parties to meet quickly and as long as necessary to get this dispute resolved," Brown said in the order.
The board will report its findings to the governor, who can then petition a court to call a 60-day cooling-off period, said Evan Westrup, a spokesman for Brown. The report will explain BART and the unions' positions, but will not find fault or issue a recommendation.
Meanwhile, commuters who rely on BART breathed a sigh of relief. Matthew Purpura, 25, commutes from San Francisco to Oakland, where he works as a coffee roaster. He said he would have borrowed his friend's car to get to work, but the commute would have been a "nightmare."
Alexis Braren, 33, commutes on BART within San Francisco, and walked three miles to her workplace when BART workers went on strike in July. BART service was shut down for four days during that strike, leading to clogged roadways and long lines for buses and ferries. Unions later agreed to call off the strike and extend their contracts until Sunday while negotiations continued.
"It made my life easier, that's for sure," Braren said about BART trains running on Monday.
Big differences remain on key issues including wages, pensions, worker safety and health care costs.
Employees with BART's two largest labour unions average about $71,000 in base salary and $11,000 in overtime annually. They pay nothing toward their pensions and a $92-a-month flat fee for health insurance, according to BART.
Brown named to the board his senior adviser Jacob Appelsmith, director of the state Department of Alcoholic Beverage Control. He also named Micki Callahan, San Francisco's director of human resources, and Robert Balgenorth, president emeritus of the State Building and Construction Trades Council of California, both who have union backgrounds.
The board will be working under the threat of a potential strike involving another Bay Area transit agency, as a union representing about 1,800 Alameda-Contra Costa Transit District bus operators, mechanics, dispatchers, and other employees gave notice of a strike Monday.
Mohajer reported from Los Angeles.